This thread is a Step-by-Step tutorial on how to properly use GroupManager, this includes how to make ranks, prefixes/suffixes, and permissions.

I will be using the group 'VIP' as a reference.

First off, you'll want to create a group, with this command:
/mangadd [GroupName]

Eg:
/mangadd VIP

This creates a whole new group, with absolutely no commands, so what you'd want to do, is allow them to have every command that the default player would have, to do this, you need to add the Default group to the VIP's group's Inheritance list.
Use this command:
/mangaddi [Group1] [Group2]

Eg:
/mangaddi VIP Default

Now the VIP group is the exact same as the Default group, but you don't want that, right? You want the VIP users to be able to have more things, like for example, a different prefix!
Say you want them to have a green Suffix saying [VIP] but the [ and ] being White, you'd want to use
This command:
/mangaddv [Group] [Variable] [value]

Eg:
/mangaddv VIP prefix &f[&2VIP&f]

Cool, right?
Now you want everyone in the VIP group to be able to do something Default users cannot do, such as have a nickname!
Use this command:
/mangaddp [Group] [Permission]

Eg:
/mangaddp VIP essentials.nickname

Now that they have a fancy nickname, they are happy!
But you don't want to have VIP anymore, so you delete it!
Use this command:
/mangdel [Group]

Eg:
/mangdel VIP

Sorry VIP, no room for you!

This concludes the Group Segment, the rest is specific users!

[=================================================================]

So there's a player that just submitted his application for Moderator, and you liked the application so much, that you want him to be a staff member now! So you'd want to
Use this command:
/manuadd [Player] [Group]

Eg:
/manuadd _Walrus_Knight_ Moderator

Now that you have your new moderator, you'd like to add specific commands for him, and just him, to use! He showed that he's a great builder with WorldEdit, so you want him to be able to use everything in WorldEdit.
Use this command:
/manuaddp [Player] [Permission]

Eg:
/manuaddp _Walrus_Knight_ worldedit.*

You now have an epic spawn that your moderator just created for you! You'd like to give him a special Suffix (Text after the player's name), you want to give him a colorful [Builder] Suffix?
Use this command:
/manuaddv [Player] [Variable] [Value]

Eg:
/manuaddv _Walrus_Knight_ suffix &f[&bBuilder&f]

Doesn't it look nice? Wait, he just griefed your spawn with WorldEdit! Remove his WorldEdit Permissions and demote him!
Use these commands:
Demote to Default:
/manuadd [Player] [Group]

Eg:
/manuadd _Walrus_Knight_ Default

Remove WorldEdit Permissions:
/manudelp [Player] [Permission]

Eg:
/manudelp _Walrus_Knight_ worldedit.*

Now don't forget to rollback your spawn using the CoreProtect plugin! (You probably want to ban that player :3)

This concludes the specific player segment

The next segment is Misc. Commands.

[=================================================================]

Want to check a player's permissions?
Use this command:
/manucheckp [Player]

Eg:
/manucheckp _Walrus_Knight_

Want to check a group's permissions?
Use this command:
/mangcheckp [Group]

Eg:
/mangcheckp VIP

Want to give a player a Group's permissions without moving him to the group?
Use this command:
/manuaddsub [Player] [Group]

Delete with:
/manudelsub [Player] [Group]

Eg:
/manuaddsub _Walrus_Knight_ VIP
/manudelsub _Walrus_Knight_ VIP

Want to delete a Group's Permissions?
Use this command:
/mangclearp [Group]

Eg:
/mangclearp VIP

[=================================================================]

This is the end of the Tutorial! Thank you for reading this and I hope it helps you set up your server! At the end of this are some helpful permissions to prevent normal players from certain things!

If you'd like to join my server, copy and paste this ip: s1.enderhosts.co.uk:30019

Permissions:
Restrict players from checking plugins:
/mangaddp default -essentials.command.plugins
(Oh, I forgot to mention, a '-' before a permission makes it so the group/player is restricted to the permission)

Allow a group to request/accept/deny teleports
/mangaddp [Group] essentials.tpa
/mangaddp [Group] essentials.tpaccept
/mangaddp [Group] essentials.tpdeny
/mangaddp [Group] essentials.tpahere

Don't forget to Diamond!
if you have any questions, please leave a comment!

Thank you all!

(This post is also on the Forums, if you'd like to go there instead!)